The military takeover in Niger has upended years of Western counterterrorism efforts in West Africa and now poses wrenching new challenges for the Biden administration’s fight against Islamist militants on the continent.

American-led efforts to degrade terrorist networks around the world have largely succeeded in longtime jihadist hot spots like Iraq, Syria, and Yemen. Not so in Africa, especially in the Sahel, the vast, semiarid region south of the Sahara where groups linked to Al Qaeda and the Islamic State are gaining ground at an alarming pace.

Niger, an impoverished nation of 25 million people that is nearly twice the size of Texas, has recently been the exception to that trend.

Terrorist attacks against civilians there decreased by 49 percent this year, largely because of the 2,600 French and American troops training and assisting Nigerien forces and a multipronged counterinsurgency strategy by the deposed president, Mohamed Bazoum, analysts say. Niger has slowed, but not stopped, a wave of extremists pushing south to coastal states.

Now all that could be in jeopardy if a regional conflict breaks out or the junta orders the Western forces, including 1,100 American troops, to leave and three U.S. drone bases — including one operated by the C.I.A. — to be shuttered.

Western-led military operations offer no silver bullet against Islamist militancy in the Sahel, now the epicenter of global militancy. The past decade of French-led operations in the region, involving thousands of troops, failed to stop thousands of attacks.

Even so, a security vacuum in Niger could embolden the militants to ramp up propaganda, increase recruitment of local and even foreign fighters, establish mini-states in remote areas, and plot attacks against Western countries. Removing the relatively small American presence would make it harder for military analysts to identify and quickly disrupt threats as they emerge, U.S. officials said.

It could also open the door to Russian influence in Niger in the form of the Kremlin-backed Wagner private military company, which already has a presence in neighboring Mali, U.S. officials say.

“The U.S. pulling out of Niger and closing its drone bases would be a devastating blow to Western counterterrorism efforts in the Sahel,” said Colin P. Clarke, a counterterrorism analyst at the Soufan Group, a security consulting firm based in New York.

The stakes in the fight are rising fast. Tens of thousands of people have died violently, and 3.3 million have fled their homes, over the past decade in Niger, Mali and Burkina Faso, which adjoin each other in West Africa. In two of them, the situation is rapidly worsening. The death toll in Mali doubled last year to about 5,000, while in Burkina Faso it rose 80 percent to 4,000, according to the Armed Conflict Location & Event Data Project. On Tuesday, 17 Nigerien soldiers were killed and 20 wounded in an ambush by armed insurgents in southwestern Niger.

The violence is spreading from those three landlocked nations toward wealthier ones along the coast of the Gulf of Guinea. Militants from Burkina Faso have carried out attacks in northern Togo and Benin.

Niger is also battling a separate Islamic State affiliate in the Lake Chad Basin, in the country’s southeast.

“Niger has been this barrier against terrorist groups for coastal countries,” said Ouhoumoudou Mahamadou, who was Niger’s prime minister until the coup and remains one of the Nigerien government officials recognized by the United States and most African nations. “With a weakened Niger, there’s little chance that this role will hold.”

The International Crisis Group has warned that the violence could also spread into Ivory Coast, one of the region’s economic powerhouses.

“All the Gulf of Guinea countries are very worried,” said Pauline Bax, deputy director of the Africa program at the International Crisis Group. Amid the furor over the coup in Niger, and the potential for Wagner to find a perch there, the regions’ Islamist groups are likely celebrating a chance to expand their hold, she said.

Niger has been a centerpiece of American efforts to combat surging Islamist militancy in the Sahel region for a decade, and has taken on greater importance since the coup in Mali.

President Barack Obama ordered the first 100 American troops to Niger in February 2013 to help set up unarmed surveillance drone operations in Niamey, the capital, to support a French-led operation combating Al Qaeda and affiliated fighters in Mali.

By 2018, the U.S. military presence had grown to 800 troops and the Pentagon was putting the finishing touches on a $110 million drone base in Agadez, in northern Niger, a major expansion of American military firepower in Africa. The risks of the growing mission were laid bare in October 2017 when a terrorist ambush killed four American soldiers, their interpreter and four Nigerien soldiers.

Niger, however, remained the main U.S. counterterrorism ally in the region under Mr. Bazoum, the country’s former interior and foreign minister, who was elected in 2021 in Niger’s first peaceful transfer of power between two democratically elected presidents since independence.

American officials praised Mr. Bazoum’s strategy, which used counterterrorism raids by American-trained commandos and some level of dialogue with local groups to address their grievances. Fewer people were killed in Niger in the first six months of this year than in the first half of any year since 2018, according to the armed conflict project.

Since the uprising on July 26, France and the European Union have suspended some aid to Niger. The U.S. secretary of state, Antony J. Blinken, has said that American security ties, worth about $500 million since 2012, were also at risk if the putsch was not reversed. The United States has suspended training and drone flights, and restricted its troops to bases. France has also suspended all joint operations with Niger’s military.

With prospects for restoring Mr. Bazoum to power appearing dim, the Biden administration is weighing two main options, officials say. It could formally declare a coup in Niger, as the administration did when military forces staged recent takeovers in Mali and Burkina Faso, which would trigger broader cuts in American aid, including military assistance. Or Washington could stop short of that designation, as it did with a military takeover in Chad, and seek an arrangement with the junta to continue counterterrorism cooperation.

So far, the situation has been relatively peaceful and has not forced the administration’s hand. But the threat of military intervention by the Economic Community of West African States, the regional bloc known as ECOWAS, and dwindling hopes of a diplomatic resolution present the Biden administration with tough choices in the coming days.

U.S. alternatives in the region are limited, officials said. The United States has conducted training exercises in Mauritania, Ghana, Chad and elsewhere in the area. But none of those countries are as centrally located as Niger, or appear likely to accept such a large American military presence. “Niger is quite a critical partner to us in the region,” Sabrina Singh, a Pentagon spokeswoman, said on Tuesday.

The United States has mainly played a supporting military role in the Sahel to France, a former colonial power. But the junta has severed military ties with France, and the recent events have highlighted the failure of France’s counterterrorism partnerships, observers say.

Underscoring the urgency of the growing crisis, Gen. Mark A. Milley, the chairman of the Joint Chiefs of Staff, spoke with his French counterpart on Wednesday to discuss the situation in Niger, a spokesman for the general said in a statement without disclosing any details of their videoconference.

The military takeover is an especially hard blow for Western interests in Niger because democracy appeared to be taking root in the country despite a history of coups and attempted coups since independence from France in 1960.

One small comfort for the Biden administration, as it attempts to balance its rejection of coups with its desire to maintain a security presence in Niger, is that the latest takeover seems to be driven more by personal or factional differences rather than any ideology.

The stunning collapse of the Western-backed, democratic government in Niger has also revived a debate about whether the security-heavy U.S. approach was flawed in the first place.

“We have an over-militarized approach to counterterrorism,” said Alexander Noyes, a political scientist at the nonprofit RAND Corporation. “And that’s hurting us.”

American aid to countries like Niger would be more effective if it prioritized support for good governance — stronger, more democratic institutions with less corruption — over the provision of lethal assistance, like drones and Special Forces, Mr. Noyes said.

West African officials have warned that the Wagner mercenary group may move to fill the void if French troops depart, amid rumors that a Nigerien junta official met recently with representatives from the paramilitary group in Mali, which has hosted about 1,500 Wagner operatives to fight off an Islamist insurgency.

Attacks against civilians in Mali have surged since the group’s arrival, as have the number of Malian refugees in neighboring countries.

U.S. officials say there is no evidence that Wagner helped instigate the military takeover in Niger, but the group is clearly trying to exploit it. “Feel free to call us anytime,” Wagner’s founder, Yevgeny V. Prigozhin, said in an audio message aimed at Niger’s junta that was shared last week on Telegram channels associated with the group.

“Niger was the last bastion of hope and security in the Sahel,” said J. Marcus Hicks, a retired two-star Air Force general who headed American Special Operations forces in Africa from 2017 to 2019. “The idea that we’d leave a vacuum for further malign Russian influence would be a real tragedy.”